In the Module Manager, the Ordering column has 'arrows' to change the ordering, but they are shaded out and not active. I *can* change the ordering of the modules if I go inside the module and change the 'Ordering' there. It does then correctly show on the Module Manager page.

If you are not sorted by the Ordering column, then you won't be able to manipulate the ordering from manager view. In Beta 5, the view was changed to hide the arrows and save order disk when not sorted by the ordering column.